WARNING: Very light spoiler regarding GONE GIRL. But written in a way that doesn't give too much away.
One of the things I struggle with (perpetually) is how to edit protagonists.
On the one hand, I like a flawed and imperfect protagonist. And books with such protagonists can be quite successful, as GONE GIRL has demonstrated (though I even wonder about this, as the "imperfect protagonist" comes about after a massive switcheroo from being a highly sympathetic protagonist). The side of me that likes new, interesting, and experimental fiction feels energized and challenged by an unlikable protagonist, and I often express impatience for protagonists who are trying to be everybody's (by which I mean, every reader's) best friend. BUT...
I'm not just an editor. I am a "reader's advocate." And I know what readers (by which I mean, the mass market) WILL and WILL NOT put up with. The protagonist is everything, really - even more so than the plot, and I'm a huge advocate of plot (I think it often doesn't get enough attention and too often takes a backseat in the genre these day). So, writers are starting with some serious strikes against them if the protagonist rubs readers the wrong way or pushes some of the wrong buttons. Here are some ways I've seen protagonists behave in recent manuscripts that have made me say: No, can't take this manuscript.
SEXIST. Sure, it was OK in the genre back in the day, but today it isn't. I think male writers think they are harkening back to the glory days of gumshoes when they have their protags comment on the bosoms of lovely ladies and call them "sweetheart," but that ship has sailed, my friends. Sexism doesn't cut it any more.
BULLYING. Nobody likes a bully. But I have seen some protags (cops, detective, etc.) engage in bullying behavior. In real life, nobody likes bullies. Nobody likes them in fiction, either.
SARCASTIC. Some writers see sarcasm as the equivalent of humor. It isn't. A protagonist who's sarcastic is generally the creation of a writer who doesn't understand how to use humor. Think about the sarcastic people in your life. Would you want to spend time with them in fiction, when you're supposed to be enjoying yourself?
UNFEELING. I'm amazed by how many protagonists encounter dead bodies but don't feel anything about the experience. Finding a dead body is a rough experience - it should engender some emotion. Often I find protagonists who use a dead body as a starting-off point without any of the messy emotional stuff that goes with it. Unfortunately, this makes the protagonist seem like an unfeeling robot.
CONDESCENDING. It's not good when a writer is condescending to readers, but it's equally bad when a protagonist is condescending to other characters. It's not uncommon for city-based protagonists to look down their noses on country folk. It's also not uncommon for rural protagonists to have a thing against urban people. Remember: Readers live in the country, in the city, and everywhere in between. You get nowhere by offending people.
POLITICALLY SNIPING. Bringing a political or religious agenda (or an anti-political or anti-religious agenda) to a protagonist can be the kiss of death. We are in the realm of mass-market genre fiction here. People don't want to hear writers bad-mouthing Republicans or Democrats, complaining about Catholicism or Judaism, Bill O'Reilly or Rachel Maddow. They want to be entertained, not annoyed by a political agenda.
SERIOUSLY MORALLY COMPROMISED. This one is tricky. A low level of being morally compromised makes for good emotional involvement. But there are certain things readers can't forgive. They won't allow a married protagonist to have an extramarital/sexual affair. They won't allow a protagonist to abandon his or her children or do anything that would put a child in danger.
I should note that letting any of these elements creep into your story, anywhere, for even a short time, can turn an editor off instantly and shut down his or her openness to the rest of the book. So, these strands need not be pervasive. If they're there, someone will grab onto them and reject the book because of it.